Method Yields Single-Cell Transcriptomes

Abstract

A new sequencing protocol is said to generate a much fuller transcriptome from single cells than was previously possible.

“There are many fundamental research questions that can only be answered by looking at single cells,” says Rickard Sandberg, PhD, a researcher at the Ludwig Institute for Cancer Research and a principal investigator at the Karolinska Institute in Stockholm. However, looking at the gene expression of single cells has been very challenging, primarily because one cell yields a very low volume of genetic material to sequence. Instead, researchers generally pool mRNA from a tissue to get an average picture of gene expression.

A new “Smart-Seq” sequencing method developed by Sandberg and his colleagues makes it possible to generate a much fuller gene-expression profile, or transcriptome, from a single cell than was previously possible. The researchers hope that the technique, described in Nature Biotechnology, will help illuminate the activities of rare cells such as circulating tumor cells, and will lead to a better understanding of heterogeneity within tumors.

To study the usefulness of the technique, the investigators studied putative circulating tumor cells captured from a melanoma patient's blood sample. Previously, it had not been proven that these rare cells, captured because they carried a membrane protein thought to be a melanoma marker, actually came from the tumor. However, the cells' transcriptomes confirmed their origin.

Following up with preliminary studies of the circulating cells, Sandberg's group found that these cells exhibited upregulated transcripts for several membrane proteins that hadn't been previously associated with melanoma. The scientists are now expanding these studies to investigate tumors from additional patients.